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BMC Biochemistry Biomed Central BMC Biochemistry BioMed Central Methodology article Open Access Displacement affinity chromatography of protein phosphatase one (PP1) complexes Greg BG Moorhead*1, Laura Trinkle-Mulcahy2, Mhairi Nimick1, Veerle De Wever1, David G Campbell3, Robert Gourlay3, Yun Wah Lam2 and Angus I Lamond2 Address: 1Department of Biological Sciences, University of Calgary, 2500 University Dr. N.W. Calgary, AB T2N 1N4, Canada, 2Wellcome Trust Biocentre, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH, UK and 3MRC Protein Phosphorylation Unit, School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK Email: Greg BG Moorhead* - [email protected]; Laura Trinkle-Mulcahy - [email protected]; Mhairi Nimick - [email protected]; Veerle De Wever - [email protected]; David G Campbell - [email protected]; Robert Gourlay - [email protected]; Yun Wah Lam - [email protected]; Angus I Lamond - [email protected] * Corresponding author Published: 10 November 2008 Received: 8 May 2008 Accepted: 10 November 2008 BMC Biochemistry 2008, 9:28 doi:10.1186/1471-2091-9-28 This article is available from: http://www.biomedcentral.com/1471-2091/9/28 © 2008 Moorhead et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Protein phosphatase one (PP1) is a ubiquitously expressed, highly conserved protein phosphatase that dephosphorylates target protein serine and threonine residues. PP1 is localized to its site of action by interacting with targeting or regulatory proteins, a majority of which contains a primary docking site referred to as the RVXF/W motif. Results: We demonstrate that a peptide based on the RVXF/W motif can effectively displace PP1 bound proteins from PP1 retained on the phosphatase affinity matrix microcystin-Sepharose. Subsequent co-immunoprecipitation experiments confirmed that each identified binding protein was either a direct PP1 interactor or was in a complex that contains PP1. Our results have linked PP1 to numerous new nuclear functions and proteins, including Ki-67, Rif-1, topoisomerase IIα, several nuclear helicases, NUP153 and the TRRAP complex. Conclusion: This modification of the microcystin-Sepharose technique offers an effective means of purifying novel PP1 regulatory subunits and associated proteins and provides a simple method to uncover a link between PP1 and additional cellular processes. Background groups based on protein sequence, catalytic signature and The phosphorylation of proteins is one of the most prev- substrate preference [3-5]. The action of protein phos- alent covalent modifications known, affecting essentially phatases is tightly controlled with cellular targeting being every aspect of cellular function [1,2]. The protein kinases an important means of regulation. Most phospho-serine and phosphatases responsible are highly conserved across and threonine dephosphorylation can be attributed to the species and, with few exceptions, the kinases belong to PPM family and the more diverse PPP family, which one large gene family while the phosphatase complement includes PP1, PP2A, PP2B, and PP4 through to PP7. PP1 is more complex and can be divided into three broad is thought to not exist as a free catalytic subunit in the cell, Page 1 of 10 (page number not for citation purposes) BMC Biochemistry 2008, 9:28 http://www.biomedcentral.com/1471-2091/9/28 but to reside in complexes with a large array of targeting addition to in vivo targeting, disrupting PP1-regulatory or regulatory subunits that define its function. Numerous subunit interactions with a peptide would be an effective PP1 docking proteins have been identified, but they most means to aid in identifying proteins in PP1 complexes and likely represent only a small fraction of the total number thus uncover new cellular processes regulated by this pro- in the cell. tein phosphatase. The microcystins are a group of cyclic peptides that bind Results and Discussion with remarkable specificity and affinity to the type one, 2A We initiated our PP1 peptide displacement study selecting and several recently identified protein phosphatases of the RVXF/W containing peptides from the PP1 targeting sub- PPP family (e.g. PP4, PP6). Microcystin covalently cou- units NIPP1 [25,30] and ZAP (ZAP3) [31,32]. They were ples to a conserved cysteine residue of PPP family mem- synthesized and tested for their ability to displace PP1 bers through its methyl-dehydroalanine residue [6,7]. binding proteins from complexes retained on the micro- Nishiwaki et al [8] first used Microcystin-Sepharose to cystin matrix. In brief, we isolated rat liver nuclei, purify PP2A. We exploited a different synthetic approach extracted proteins and incubated extracts with Microcys- whereby the carbon-carbon double bond of methyl-dehy- tin-Sepharose to bind the microcystin-sensitive protein droalanine in microcystin couples the latter to ami- phosphatases [31]. After extensive column washing, we noethanethiol, which is then linked to a Sepharose bead. incubated the matrix with the NIPP1 or ZAP peptides This generates a high affinity binding matrix for the (RPKRKRKNSRVTFSEDDEII and GKKRVRWADLE, microcystin-sensitive protein phosphatases that does not respectively) to selectively displace proteins retained on covalently couple the phosphatase [6]. Microcystin- the matrix through PP1. This implies that PP1 itself and Sepharose has proved to be a powerful tool to purify these other microcystin-sensitive phosphatase complexes protein phosphatases and their associated regulatory sub- should be retained on the matrix and can subsequently be units from a variety of tissues and cell types [9-12]. eluted with the chaotrophic agent sodium thiocyanate (NaSCN), which will also displace other bound proteins With only a few characterized exceptions, PP1 interacting [9] including some that may be retained by binding non- proteins bind PP1 through their primary docking specifically to the Sepharose bead. Blotting for PP1 and sequence called the RVXF/W motif [13]. Their molecular the PP2A regulatory subunit PR65 show this to be true interaction with PP1 has been visualized via PP1-peptide (Figure 1a and 1b) with no retention of these phosphatase and PP1 regulatory subunit structures [14,15]. It has also subunits on a control matrix coupled with Tris alone. The emerged that additional or secondary interaction sites NIPP1 peptide (RPKRKRKNSRVTFSEDDEII) readily dis- often play a role in binding PP1 and likely contribute to placed PP1 regulatory subunits (data not shown), yet we PP1 isoform specificity recognition, substrate docking and chose to continue working with the ZAP peptide modulation of PP1 activity [13,15-20]. Based on a compi- (GKKRVRWADLE, later also referred to as RVRW peptide) lation of demonstrated RVXF/W interaction motifs [21- because it is small, readily soluble and an excellent match 23], the panning of a random peptide library [24], and to the optimal PP1 binding peptide discovered through mutagenesis and modeling studies [23] we noted prefer- panning a random peptide library [24]. Indeed, the ZAP ences for particular amino acids within and adjacent to peptide RVRW motif and the additional C-terminal the RVXF/W motif. This led us to speculate that a PP1 amino acids ADL and N-terminal basic amino acids (KK) interaction motif peptide, based on this comparison, were most frequently obtained in the random peptide could be a unique means to specifically disrupt PP1-tar- library screen (Figure 2 in [24]). We thus predict that the getting or regulatory subunit interactions [14,25,26]. ZAP sequence GKKRVRWADLE is the most suitable, high Slight variation in the RVXF/W-motif combined with the affinity peptide that will compete and displace most other now recognized additional, secondary PP1 interaction proteins docked to PP1 through variations of the RVXF/ sites provide sufficient interaction specificity which may W-motif. We acknowledge that even with an 'optimal allow the development of drugs or peptide mimetics to binding peptide' there are certainly other PP1 interacting abolish specific PP1 binding protein interactions in vivo. proteins on the matrix that may not be displaced because The idea of targeting protein-protein interaction domains of completely novel PP1 interaction sites and/or addi- with drugs has historically not been favored by the phar- tional interaction sites outside of the RVXF/W-motif [20] maceutical industry yet, due to improved understanding that could maintain the interaction with PP1 even if the of the underlying molecular mechanisms, it is now a con- RVXF/W site is displaced. Thus, the PP1 binding partners cept that is growing in popularity [27,28]. This idea has uncovered here still most likely only represent a sub-pop- been explored with PKA anchoring proteins (AKAPs) ulation of the total nuclear PP1 binding partners. where optimal RI and RII subunit binding peptides were derived from parent peptides and used to target PKA in RVRW peptide eluted samples were blotted for the known vivo and displace it from its normal anchoring site [29]. In nuclear PP1 binding proteins ZAP, p99 (PNUTS) and Page 2 of 10 (page number not for citation purposes) BMC Biochemistry 2008, 9:28 http://www.biomedcentral.com/1471-2091/9/28 Figure 1 A peptide based on the PP1 interaction motif RVXF/W displaces PP1 regulatory subunits from the affinity matrix microcystin-Sepharose. Proteins extracted from isolated rat liver nuclei were incubated with the affinity (MC) or control (Con) matrix (Tris coupled). Proteins were displaced with the RPKRKRKNSRVTFSEDDEII peptide (a), while in (b), elution was performed with either RPKRKRKNSRVTFSEDDEII or GKKRVRWADLE prior to the 3 M NaSCN elution. The control matrix is only used in the panel (a) experiment while microcystin-Sepharose is used in all others. After concentration, samples were run on 10% SDS-PAGE, blotted to nitrocellulose and membranes were probed with anti-PR65 and PP1 antibod- ies.
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